[galaxy-user] Bowtie reference genome

2012-05-14 Thread Fang, Xiefan 
Dear galaxy users,
   I am trying to map some multiplexing bisulfite PCR data (Illumina) to 
our 20+ genes of interest. I want to use the Map with Bowtie for Illumina in 
Galaxy. Therefore, I need to change the reference genome to my known DNA 
sequences. However, I don't know how to make such a reference index. Shall it 
be in FASTQ, FASTA or CTF format? My reference sequences are now in a word 
file. How can I convert their format to the desired one?
  My second question is that my sequencing data for an individual sample 
are separated in 8 different FASTQ files. Does it matter that I map them 
individually and then merge them together? Or shall I combine them first (which 
will be a very huge file) and then do the mapping? Does it change the results 
either way?
  My last question is that since we are looking at the CG methylation, 
there certainly will be mismatches in the CG sites (such as being a CG or TG) 
compared to the reference sequence. I am afraid the mismatches may be greater 
than 3 for a read about 100 bp. Do you think Bowtie will allow these many 
mismatches? If so, can you suggest a better way to do the mapping?

Thanks for your attention!!!
Xiefan

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Re: [galaxy-user] GCC2012 Update

2012-05-14 Thread Dave Clements 
Hello all,

The original email included a link to register for GCC2011.  While, gosh,
that was a great meeting, it might have been more helpful to provide you
with the link to this year's registration link instead:

  http://wiki.g2.bx.psu.edu/Events/GCC2012/Register

With apologies for the duplicate emails,

Dave C.


On Mon, May 14, 2012 at 1:13 PM, Dave Clements
cleme...@galaxyproject.orgwrote:

 Hello all,

 The 2012 Galaxy Community Conference (GCC2012), being held in Chicago,
 Illinois, July 25-27, is *now just 10 weeks away*.  We have updates on:

 1. Help set the topics covered on Training Day (by this Friday)
 2. Early registration closes June 11
 3. Confirmed Speaker List

 As always, please let me know if you have any questions, and I hope to see
 you in Chicago!

 Thanks,

 Dave Clements
 on behalf of the GCC2012 Organizing Committee


 *1. Training Day Topics: Vote by this Friday
 *
 A day of tutorials has been added to the agenda this year.  The GCC2012
 Training Day has 3 parallel tracks, each featuring four, 90 minute
 workshops and covering between and 7 and 12 different topics.  *Please
 take a few minutes to vote on topics that you would like to see presented:
 *  http://bit.ly/GCC2012TDSurvey

 The survey ends this Friday, May 18, so please provide your feedback now.


 *2. Early Registration: Ends June 11
 *
 The GCC2012 early registration is now just 4 weeks away.  Registering
 early saves* 36 to 42%* on registration costs, and allows you to book
 discounted conference lodging before it fills up.  *Register now at*
   http://galaxy.psu.edu/gcc2011/Register.html


 *3. Confirmed Speakers and Abstracts Posted
 *
 A list of confirmed speakers and abstracts are now available on the
 conference web site at
   http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers

 This list is not yet finished, but will give you a pretty accurate idea of
 the range of topics that will be discussed during the main meeting.


 --
 http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012
 http://galaxyproject.org/
 http://getgalaxy.org/
 http://usegalaxy.org/
 http://galaxyproject.org/wiki/




-- 
http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
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